Execute command reference

The execute command provides tools to execute CWL documents locally or on a remote server.

Execution of CWL Files locally or on remote servers

Usage: s4n execute <COMMAND>

Commands:
  local          Runs CWL files locally [aliases: l]
  remote         Runs CWL files remotely using reana [aliases: r]
  make-template  Creates job file template for execution (e.g. inputs.yaml)
  help           Print this message or the help of the given subcommand(s)

Options:
  -h, --help  Print help

`execute local`

This command executes a given CWL File on the local machine (without the need of CWLTool).

Runs CWL files locally

Usage: s4n execute local [OPTIONS] <FILE> [ARGS]...

Arguments:
  <FILE>     CWL File to execute
  [ARGS]...  Other arguments provided to cwl file

Options:
      --outdir <OUT_DIR>  A path to output resulting files to
      --quiet             Runner does not print to stdout
      --podman            Use podman instead of docker
  -h, --help              Print help

`execute remote`

This command will communicate with a given REANA server and schedule an execution.

Runs CWL files remotely using reana

Usage: s4n execute remote <COMMAND>

Commands:
  start     Schedules Execution on REANA
  status    Get the status of Execution on REANA
  download  Downloads finished Workflow from REANA
  rocrate   Downloads finished Workflow Run RO-Crate from REANA
  logout    Delete reana information from credential storage (a.k.a logout)
  help      Print this message or the help of the given subcommand(s)

Options:
  -h, --help  Print help

`execute make-template`

s4n execute make-template is able to create a dummy CWL job file (e.g. inputs.yaml) that can be used as a template for an upoming execution of CWL.

Creates job file template for execution (e.g. inputs.yaml)

Usage: s4n execute make-template <CWL>

Arguments:
  <CWL>  CWL File to create input template for

Options:
  -h, --help  Print help